[Fis] Fw: "Mechanical Information" in DNA

Joseph Brenner joe.brenner at bluewin.ch
Thu Jun 9 11:10:18 CEST 2016


Dear Folks,

In my humble opinion, "Mechanical Information" is a contradiction in terms when applied to biological processes as described, among others, by Bob L. and his colleagues. When applied to isolated DNA, it gives at best a reductionist perspective. In the reference cited by Hector, the word 'mechanical' could be dropped or replaced by spatial without affecting the meaning.

Best,

Joseph

----- Original Message ----- 
From: Bob Logan 
To: Moisés André Nisenbaum 
Cc: fis 
Sent: Thursday, June 09, 2016 4:04 AM
Subject: Re: [Fis] "Mechanical Information" in DNA


Thanks to Moises for the mention of my paper with Stuart Kauffman. If anyone is interested in reading it one can find it at the following Web site:


https://www.academia.edu/783503/Propagating_organization_an_enquiry


Here is the abstract:


Propagating Organization: An Inquiry. 
Stuart Kauffman, Robert K. Logan, Robert Este, Randy Goebel, David Hobill and Ilya Smulevich. 

2007. Biology and Philosophy 23: 27-45.

Abstract 

Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection – and perhaps self-organization - could occur on many worlds via different causal mechanisms.

Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere.

Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe.


 








______________________


Robert K. Logan
Prof. Emeritus - Physics - U. of Toronto 
Fellow University of St. Michael's College
Chief Scientist - sLab at OCAD
http://utoronto.academia.edu/RobertKLogan
www.physics.utoronto.ca/Members/logan
www.researchgate.net/profile/Robert_Logan5/publications




On Jun 8, 2016, at 4:40 PM, Moisés André Nisenbaum <moises.nisenbaum en ifrj.edu.br> wrote:


Hi, John. It is amazing!!
I would like to highlight the word "constraints" at the caption of the DNA diagram (http://phys.org/news/2016-06-layer-dna.html)
"The rigid base-pair model is forced, using 28 constraints (indicated by red spheres), into a lefthanded superhelical path that mimics the DNA conformation in the nucleosome. Credit: Leiden Institute of Physics"
The same word is used by Bob Logan and Stuart Kauffman to relate mechanical concepts with 'information' (http://philpapers.org/rec/KAUPOA)
Could it have any parallel between these two approaches?


Also, you usually think "DNA" associated with Biological Sciences, but this research is made at Leiden Institute of Physics! Of course, to work current (complex, innovative) science you must have an interdisciplinary approach.


Abraço.


Moisés


2016-06-08 16:40 GMT-03:00 John Collier <Collierj en ukzn.ac.za>:

  A previously hypothesized “second layer” of information in DNA may have been isolated.



  http://phys.org/news/2016-06-layer-dna.html



  John Collier

  Professor Emeritus and Senior Research Associate

  University of KwaZulu-Natal

  http://web.ncf.ca/collier




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Moisés André Nisenbaum
Doutorando IBICT/UFRJ. Professor. Msc.
Instituto Federal do Rio de Janeiro - IFRJ
Campus Rio de Janeiro
moises.nisenbaum en ifrj.edu.br
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